5CDW

Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.602 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and biophysical investigation of the interaction of a mutant Grb2 SH2 domain (W121G) with its cognate phosphopeptide.

Papaioannou, D.Geibel, S.Kunze, M.B.Kay, C.W.Waksman, G.

(2016) Protein Sci. 25: 627-637

  • DOI: 10.1002/pro.2856

  • PubMed Abstract: 
  • The adaptor protein Grb2 is a key element of mitogenetically important signaling pathways. With its SH2 domain it binds to upstream targets while its SH3 domains bind to downstream proteins thereby relaying signals from the cell membranes to the nucl ...

    The adaptor protein Grb2 is a key element of mitogenetically important signaling pathways. With its SH2 domain it binds to upstream targets while its SH3 domains bind to downstream proteins thereby relaying signals from the cell membranes to the nucleus. The Grb2 SH2 domain binds to its targets by recognizing a phosphotyrosine (pY) in a pYxNx peptide motif, requiring an Asn at the +2 position C-terminal to the pY with the residue either side of this Asn being hydrophobic. Structural analysis of the Grb2 SH2 domain in complex with its cognate peptide has shown that the peptide adopts a unique β-turn conformation, unlike the extended conformation that phosphopeptides adopt when bound to other SH2 domains. TrpEF1 (W121) is believed to force the peptide into this unusual conformation conferring this unique specificity to the Grb2 SH2 domain. Using X-ray crystallography, electron paramagnetic resonance (EPR) spectroscopy, and isothermal titration calorimetry (ITC), we describe here a series of experiments that explore the role of TrpEF1 in determining the specificity of the Grb2 SH2 domain. Our results demonstrate that the ligand does not adopt a pre-organized structure before binding to the SH2 domain, rather it is the interaction between the two that imposes the hairpin loop to the peptide. Furthermore, we find that the peptide adopts a similar structure when bound to both the wild-type Grb2 SH2 domain and a TrpEF1Gly mutant. This suggests that TrpEF1 is not the determining factor for the conformation of the phosphopeptide.


    Organizational Affiliation

    UCL And Birkbeck, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, United Kingdom.,London Centre for Nanotechnology, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom.,Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2, Haus D15, Würzburg, 97080, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth factor receptor-bound protein 2
A, E, B, C, G, H, K, L, O, P, U, V, Y, Z, c, d
100Homo sapiensMutation(s): 1 
Gene Names: GRB2 (ASH)
Find proteins for P62993 (Homo sapiens)
Go to Gene View: GRB2
Go to UniProtKB:  P62993
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SER-PTR-VAL-ASN-VAL-GLN
D, M, s, a, F, J, N, R, T, X, b, f, h, j, I, Q
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
a, b, D, f, F, h, I, J, j, M, N, Q, R, s, T, X
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.602 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.650α = 90.00
b = 72.140β = 93.31
c = 172.140γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release